5GSM

Glycoside hydrolase B with product


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.130 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Glycoside hydrolase B with product

Watanabe, M.Kamachi, S.Mine, S.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exo-beta-D-glucosaminidase
A, B
786Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)Mutation(s): 0 
Gene Names: Tk-Glm
Find proteins for Q76HN4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Go to UniProtKB:  Q76HN4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCS
Query on GCS

Download SDF File 
Download CCD File 
A, B
D-GLUCOSAMINE
2-AMINO-2-DEOXY-D-GLUCOSE
C6 H13 N O5
MSWZFWKMSRAUBD-QZABAPFNSA-N
 Ligand Interaction
B3P
Query on B3P

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Download CCD File 
A
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
 Ligand Interaction
PPI
Query on PPI

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Download CCD File 
A, B
PROPANOIC ACID
C3 H6 O2
XBDQKXXYIPTUBI-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.130 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 76.585α = 90.00
b = 119.991β = 98.66
c = 85.902γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Japan Society for the Promotion of SciencesJapan25450143

Revision History 

  • Version 1.0: 2017-02-01
    Type: Initial release